Phusion requires that the primers are phosphorylated for mutagensis to work, unlike Pfu. If you cannot phosphorylate them use Pfu as recommended by Charlotte
Not really. Phusion *protocol* requires phosphorylated primers but seemingly the only reason for that is that they needed to find a way to bypass Stratagene's patent on "QuikChange" protocol. There is quite obviously no need for ligation at all as evidenced by any QuikChange reaction. (Even more, there is no need for two primers! We *only* ever use a single primer and the frequency of positive clones is the same).
As for the Pfu, there are now much better derivatives of it than the good old Turbo. "Ultra" has lower mutation rate and "Ultra Fusion II" is a lot better in every respect (and in our hands significantly better than Phusion).
- Dima
